Mercurial > repos > sanbi-uwc > novo_align
changeset 28:395aac51afa6 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 1d2ba43f108038467c4b0b145ae3887e8f152f33
author | sanbi-uwc |
---|---|
date | Tue, 29 May 2018 09:30:58 -0400 |
parents | df170f4d2eea |
children | 8ed9bca55370 |
files | novo_align.py |
diffstat | 1 files changed, 1 insertions(+), 1 deletions(-) [+] |
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--- a/novo_align.py Mon May 07 09:42:08 2018 -0400 +++ b/novo_align.py Tue May 29 09:30:58 2018 -0400 @@ -10,7 +10,7 @@ def novo_align(output_filename, index_filename, fwd_file, rev_file ): param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA' - cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools sort - | samtools view -b - > {}".format( + cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format( index_filename, fwd_file, rev_file,